PerlPrimer is a free, open-source GUI application written in Perl 
that designs primers for standard PCR, bisulphite PCR, real-time PCR 
(QPCR) and sequencing. It aims to automate and simplify the process 
of primer design. 

PerlPrimer's current features include the following:

- Calculation of possible primer-dimers
- Retrieval of genomic or cDNA sequences from Ensembl (including both 
  sequences automatically for QPCR)
- Ability to BLAST search primers using the NCBI server or a local 
  server
- Results can be saved or optionally exported in a tab-delimited 
  format that is compatible with most spreadsheet applications.
- ORF and CpG island detection algorithms
- Ability to add cloning sequences to primers, automatically adjusted 
  to be in-frame
- QPCR primer design without manual intron-exon boundary entry 

For details and citation:
Marshall OJ. PerlPrimer: cross-platform, graphical primer design for 
standard, bisulphite and real-time PCR. Bioinformatics 2004 
20(15):2471-2472

This requires perl-tk and libwww-perl. For Real Time PCR, spidey is 
required. 
